Data-driven crop growth simulation on time-varying generated images using multi-conditional generative adversarial networks.

BACKGROUND: Image-based crop growth modeling can substantially contribute to precision agriculture by revealing spatial crop development over time, which allows an early and location-specific estimation of relevant future plant traits, such as leaf area or biomass. A prerequisite for realistic and sharp crop image generation is the integration of multiple growth-influencing conditions in a model, such as an image of an initial growth stage, the associated growth time, and further information about the field treatment. While image-based models provide more flexibility for crop growth modeling than process-based models, there is still a significant research gap in the comprehensive integration of various growth-influencing conditions. Further exploration and investigation are needed to address this gap. METHODS: We present a two-stage framework consisting first of an image generation model and second of a growth estimation model, independently trained. The image generation model is a conditional Wasserstein generative adversarial network (CWGAN). In the generator of this model, conditional batch normalization (CBN) is used to integrate conditions of different types along with the input image. This allows the model to generate time-varying artificial images dependent on multiple influencing factors. These images are used by the second part of the framework for plant phenotyping by deriving plant-specific traits and comparing them with those of non-artificial (real) reference images. In addition, image quality is evaluated using multi-scale structural similarity (MS-SSIM), learned perceptual image patch similarity (LPIPS), and Fréchet inception distance (FID). During inference, the framework allows image generation for any combination of conditions used in training; we call this generation data-driven crop growth simulation. RESULTS: Experiments are performed on three datasets of different complexity. These datasets include the laboratory plant Arabidopsis thaliana (Arabidopsis) and crops grown under real field conditions, namely cauliflower (GrowliFlower) and crop mixtures consisting of faba bean and spring wheat (MixedCrop). In all cases, the framework allows realistic, sharp image generations with a slight loss of quality from short-term to long-term predictions. For MixedCrop grown under varying treatments (different cultivars, sowing densities), the results show that adding these treatment information increases the generation quality and phenotyping accuracy measured by the estimated biomass. Simulations of varying growth-influencing conditions performed with the trained framework provide valuable insights into how such factors relate to crop appearances, which is particularly useful in complex, less explored crop mixture systems. Further results show that adding process-based simulated biomass as a condition increases the accuracy of the derived phenotypic traits from the predicted images. This demonstrates the potential of our framework to serve as an interface between a data-driven and a process-based crop growth model. CONCLUSION: The realistic generation and simulation  of future plant appearances is adequately feasible by multi-conditional CWGAN. The presented framework complements process-based models and overcomes their limitations, such as the reliance on assumptions and the low exact field-localization specificity, by realistic visualizations of the spatial crop development that directly lead to a high explainability of the model predictions.

A model for colour preference behaviour of spring migrant aphids.

Aphids are economically and ecologically important herbivorous insects. A critical step in their life cycle is the visually guided host finding behaviour. To elucidate the role of colour in host finding of aphid spring migrants we conducted large colour trap experiments in the field and analysed aphid catch data, using trap spectral reflectance data as input. Based on known and putative photoreceptor sensitivities we developed and optimized a simple empirical colour choice model for spring migrants of different aphid species which confirmed and explained the yellow preference of these insects. In a further step, we applied multivariate statistical methods to behavioural and reflectance data, but without data on photoreceptor sensitivities, to find the wavelengths of greatest importance for the aphids' behavioural responses. This analysis confirmed the position of the green photoreceptor peak previously obtained independently with electrophysiological methods. In a final step, we applied the colour preference model to a dataset of leaf spectra. This showed that aphid visual preference would be dependent on the plants' nutritional status, with lower nitrogen input being associated with stronger preference, despite known benefits of high nitrogen levels for aphid reproduction and fitness. Ecological and evolutionary implications of these results are discussed. This article is part of the theme issue 'Understanding colour vision: molecular, physiological, neuronal and behavioural studies in arthropods'.

Mixture × Genotype Effects in Cereal/Legume Intercropping.

Cropping system diversification through annual intercropping provides a pathway for agricultural production with reduced inputs of fertilizer and pesticides. While several studies have shown that intercrop performance depends on the genotypes used, the available evidence has not been synthesized in an overarching analysis. Here, we review the effects of genotypes in cereal/legume intercropping systems, showing how genotype choice affects mixture performance. Furthermore, we discuss the mechanisms underlying the interactions between genotype and cropping system (i.e., sole cropping vs. intercropping). Data from 69 articles fulfilling inclusion criteria were analyzed, out of which 35 articles reported land equivalent ratio (LER), yielding 262 LER data points to be extracted. The mean and median LER were 1.26 and 1.24, respectively. The extracted genotype × cropping system interaction effects on yield were reported in 71% out of 69 publications. Out of this, genotype × cropping system interaction effects were significant in 75%, of the studies, whereas 25% reported non-significant interactions. The remaining studies did not report the effects of genotype × cropping system. Phenological and morphological traits, such as differences in days to maturity, plant height, or growth habit, explained variations in the performance of mixtures with different genotypes. However, the relevant genotype traits were not described sufficiently in most of the studies to allow for a detailed analysis. A tendency toward higher intercropping performance with short cereal genotypes was observed. The results show the importance of genotype selection for better in cereal/legume intercropping. This study highlights the hitherto unrevealed aspects of genotype evaluation for intercropping systems that need to be tackled. Future research on genotype effects in intercropping should consider phenology, root growth, and soil nutrient and water acquisition timing, as well as the effects of weeds and diseases, to improve our understanding of how genotype combination and breeding may help to optimize intercropping systems.

Remineralizing soils? The agricultural usage of silicate rock powders: A review.

Soil nutrient depletion threatens global food security and has been seriously underestimated for potassium (K) and several micronutrients. This is particularly the case for highly weathered soils in tropical countries, where classical soluble fertilizers are often not affordable or not accessible. One way to replenish macro- and micronutrients are ground silicate rock powders (SRPs). Rock forming silicate minerals contain most nutrients essential for higher plants, yet slow and inconsistent weathering rates have restricted their use in the past. Recent findings, however, challenge past agronomic objections which insufficiently addressed the factorial complexity of the weathering process. This review therefore first presents a framework with the most relevant factors for the weathering of SRPs through which several outcomes of prior studies can be explained. A subsequent analysis of 48 crop trials reveals the potential as alternative K source and multi-nutrient soil amendment for tropical soils, whereas the benefits for temperate soils are currently inconclusive. Beneficial results prevail for mafic and ultramafic rocks like basalts and rocks containing nepheline or glauconite. Several rock modifications are highly efficient in increasing the agronomic effectiveness of SRPs. Enhanced weathering of SRPs could additionally sequester substantial amounts of CO2 from the atmosphere and silicon (Si) supply can induce a broad spectrum of plant biotic and abiotic stress resistance. Recycling massive amounts of rock residues from domestic mining industries could furthermore resolve serious disposal challenges and improve fertilizer self-sufficiency. In conclusion, under the right circumstances, SRPs could not only advance low-cost and regional soil sustaining crop production but contribute to various sustainable development goals.

Upper limits to sustainable organic wheat yields.

Current use of mineral nitrogen (N) fertilizers is unsustainable because of its high fossil energy requirements and a considerable enrichment of the biosphere with reactive N. Biological nitrogen fixation (BNF) from leguminous crops is the most important renewable primary N source, especially in organic farming. However, it remains unclear to which degree BNF can sustainably replace mineral N, overcome the organic to conventional (O:C) yield gap and contribute to food security. Using an agronomic modelling approach, we show that in high-yielding areas farming systems exclusively based on BNF are unlikely to sustainably reach yield levels of mineral-N based systems. For a high reference wheat yield (7.5 t ha-1) and a realistic proportion of fodder legumes in the rotation (33%) even optimistic levels of BNF (282 kg N ha-1), resulted in an O:C ratio far below parity (0.62). Various constraints limit the agricultural use of BNF, such as arable land available for legumes and highly variable performance under on-farm conditions. Reducing the O:C yield gap through legumes will require BNF performance to be increased and N losses to be minimised, yet our results show that limits to the productivity of legume-based farming systems will still remain inevitable.

Crop Resilience to Drought With and Without Response Diversity.

In the face of increasingly frequent droughts threatening crop performance, ecological theory suggests that higher species diversity may help buffering productivity by making systems more resistant through resource complementarity and more resilient through higher response diversity. However, empirical evidence for these diversity effects under drought stress has remained patchy. In two pot experiments, we explored whether mixing two legume species with a contrasting response to water availability, alsike clover (AC) and black medic (BM), promotes resistance to cumulative drought stress, and resilience of aboveground crop biomass to a transient drought event. The mixture was more productive than the average of the sole crops, and this mixture effect was higher in the non-stressed than in the drought-stressed plants. However, with six levels of constant drought intensities, the mixture effect was not consistently affected by drought level. Response diversity was evident as asynchrony of growth in the two species after the drought event, with BM re-growing faster than AC. Significant resilience to drought was observed in sole AC, i.e., without response diversity. Resilience was larger in AC than in BM and increased from 44 to 72 days after sowing (DAS). The mixture was more resilient than the average resilience of the sole crops at 72 DAS, but it was never more resilient than AC, indicating that resilience is promoted by, but not dependent on response diversity. We conclude that crop diversity may contribute to drought resilience through growth asynchrony, but that species identity plays a crucial role in making systems more drought-resilient.

Natural Selection Towards Wild-Type in Composite Cross Populations of Winter Wheat.

Most of our crops are grown in monoculture with single genotypes grown over wide acreage. An alternative approach, where segregating populations are used as crops, is an exciting possibility, but outcomes of natural selection upon this type of crop are not well understood. We tracked allelic frequency changes in evolving composite cross populations of wheat grown over 10 generations under organic and conventional farming. At three generations, each population was genotyped with 19 SSR and 8 SNP markers. The latter were diagnostic for major functional genes. Gene diversity was constant at SSR markers but decreased over time for SNP markers. Population differentiation between the four locations could not be detected, suggesting that organic vs. non-organic crop management did not drive allele frequency changes. However, we did see changes for genes controlling plant height and phenology in all populations independently and consistently. We interpret these changes as the result of a consistent natural selection towards wild-type. Independent selection for alleles that are associated with plant height suggests that competition for light was central, resulting in the predominance of stronger intraspecific competitors, and highlighting a potential trade-off between individual and population performance.

Grain legume yields are as stable as other spring crops in long-term experiments across northern Europe.

Grain legumes produce high-quality protein for food and feed, and potentially contribute to sustainable cropping systems, but they are grown on only 1.5% of European arable land. Low temporal yield stability is one of the reasons held responsible for the low proportion of grain legumes, without sufficient quantitative evidence. The objective of this study was to compare the yield stability of grain legumes with other crop species in a northern European context and accounting for the effects of scale in the analysis and the data. To avoid aggregation biases in the yield data, we used data from long-term field experiments. The experiments included grain legumes (lupin, field pea, and faba bean), other broad-leaved crops, spring, and winter cereals. Experiments were conducted in the UK, Sweden, and Germany. To compare yield stability between grain legumes and other crops, we used a scale-adjusted yield stability indicator that accounts for the yield differences between crops following Taylor's Power Law. Here, we show that temporal yield instability of grain legumes (30%) was higher than that of autumn-sown cereals (19%), but lower than that of other spring-sown broad-leaved crops (35%), and only slightly greater than spring-sown cereals (27%). With the scale-adjusted yield stability indicator, we estimated 21% higher yield stability for grain legumes compared to a standard stability measure. These novel findings demonstrate that grain legume yields are as reliable as those of other spring-sown crops in major production systems of northern Europe, which could influence the current negative perception on grain legume cultivation. Initiatives are still needed to improve the crops agronomy to provide higher and more stable yields in future.

Is there sufficient Ensifer and Rhizobium species diversity in UK farmland soils to support red clover (Trifolium pratense), white clover (T. repens), lucerne (Medicago sativa) and black medic (M. lupulina)?

Rhizobia play important roles in agriculture owing to their ability to fix nitrogen through a symbiosis with legumes. The specificity of rhizobia-legume associations means that underused legume species may depend on seed inoculation with their rhizobial partners. For black medic (Medicago lupulina) and lucerne (Medicago sativa) little is known about the natural prevalence of their rhizobial partner Ensifer meliloti in UK soils, so that the need for inoculating them is unclear. We analysed the site-dependence of rhizobial seed inoculation effects on the subsequent ability of rhizobial communities to form symbioses with four legume species (Medicago lupulina, M. sativa, Trifolium repens and T. pratense). At ten organic farms across the UK, a species-diverse legume based mixture (LBM) which included these four species was grown. The LBM seed was inoculated with a mix of commercial inocula specific for clover and lucerne. At each site, soil from the LBM treatment was compared to the soil sampled prior to the sowing of the LBM (the control). From each site and each of the two treatments, a suspension of soils was applied to seedlings of the four legume species and grown in axenic conditions for six weeks. Root nodules were counted and their rhizobia isolated. PCR and sequencing of a fragment of the gyrB gene from rhizobial isolates allowed identification of strains. The number of nodules on each of the four legume species was significantly increased when inoculated with soil from the LBM treatment compared to the control. Both the proportion of plants forming nodules and the number of nodules formed varied significantly by site, with sites significantly affecting the Medicago species but not the Trifolium species. These differences in nodulation were broadly reflected in plant biomass where site and treatment interacted; at some sites there was a significant advantage from inoculation with the commercial inoculum but not at others. In particular, this study has demonstrated the commercial merit of inoculation of lucerne with compatible rhizobia.

Boxwood Borer Heterobostrychus brunneus (Coleoptera: Bostrichidae) Infesting Dried Cassava: A Current Record from Southern Ethiopia.

Insect specimens of adult beetles and larvae of 7-9 and 9-10 mm length, respectively were collected from infested dry cassava at two locations from multiple stores in southern Ethiopia. The specimens were identified as Heterobostrychus brunneus (Murray, 1867) commonly known as boxwood borer and auger beetle. The study presents a current record of H. brunneus in Ethiopia, particularly in the context of infesting food products. Additionally, a wide geographical distribution of the pest was reviewed and presented in this article. Current evidence suggests that H. brunneus is a serious pest of forest wood, structural timbers, and dried food products and that it carries a risk to be introduced into various other parts of the world via global trade.

Resilience as a universal criterion of health.

To promote and maintain health in agricultural and food systems, appropriate criteria are needed for the description and assessment of the health of soils, plants, animals, humans and ecosystems. Here we identify the concept of resilience as a universally applicable and fundamentally important criterion of health in all relevant areas of agriculture. We discuss definitions of resilience for soils, plants, animals, humans and ecosystems, and explore ways in which resilience can be applied as a criterion of health in different agricultural contexts. We show how and why resilience can be seen as a key criterion of health. Based on this, we discuss how resilience can be used as a link between soil, plant, animal, human and ecosystem health. Finally, we highlight four key areas for future research on resilience in agriculture, namely spatial and temporal scaling of resilience; effects of diversity; the role of networks for resilience; and stakeholder involvement.

Assessing health in agriculture--towards a common research framework for soils, plants, animals, humans and ecosystems.

In agriculture and food systems, health-related research includes a vast diversity of topics. Nutritional, toxicological, pharmacological, epidemiological, behavioural, sociological, economic and political methods are used to study health in the five domains of soils, plants, livestock, humans and ecosystems. An idea developed in the early founding days of organic agriculture stated that the health of all domains is one and indivisible. Here we show that recent research reveals the existence and complex nature of such health links among domains. However, studies of health aspects in agriculture are often separated by disciplinary boundaries. This restrains the understanding of health in agricultural systems. Therefore we explore the opportunities and limitations of bringing perspectives together from the different domains. We review current approaches to define and assess health in agricultural contexts, comparing the state of the art of commonly used approaches and bringing together the presently disconnected debates in soil science, plant science, veterinary science and human medicine. Based on a qualitative literature analysis, we suggest that many health criteria fall into two paradigms: (1) the Growth Paradigm, where terms are primarily oriented towards continued growth; (2) the Boundary Paradigm, where terms focus on maintaining or coming back to a status quo, recognising system boundaries. Scientific health assessments in agricultural and food systems need to be explicit in terms of their position on the continuum between Growth Paradigm and Boundary Paradigm. Finally, we identify areas and concepts for a future direction of health assessment and research in agricultural and food systems.

Seasonal phenology and species composition of the aphid fauna in a northern crop production area.

BACKGROUND: The species diversity of aphids and seasonal timing of their flight activity can have significant impacts on crop production, as aphid species differ in their ability to transmit plant viruses and flight timing affects virus epidemiology. The aim of the study was to characterise the species composition and phenology of aphid fauna in Finland in one of the northernmost intensive crop production areas of the world (latitude 64°). METHODOLOGY/PRINCIPAL FINDINGS: Flight activity was monitored in four growing seasons (2007-010) using yellow pan traps (YPTs) placed in 4-8 seed potato fields and a Rothamsted suction trap. A total of 58,528 winged aphids were obtained, identified to 83 taxa based on morphology, and 34 species were additionally characterised by DNA barcoding. Seasonal flight activity patterns analysed based on YPT catch fell into three main phenology clusters. Monoecious taxa showed early or middle-season flight activity and belonged to species living on shrubs/trees or herbaceous plants, respectively. Heteroecious taxa occurred over the entire potato growing season (ca. 90 days). Abundance of aphids followed a clear 3-year cycle based on suction trap data covering a decade. Rhopalosiphum padi occurring at the end of the potato growing season was the most abundant species. The flight activity of Aphis fabae, the main vector of Potato virus Y in the region, and Aphis gossypii peaked in the beginning of potato growing season. CONCLUSIONS/SIGNIFICANCE: Detailed information was obtained on phenology of a large number aphid species, of which many are agriculturally important pests acting as vectors of plant viruses. Aphis gossypii is known as a pest in greenhouses, but our study shows that it occurs also in the field, even far in the north. The novel information on aphid phenology and ecology has wide implications for prospective pest management, particularly in light of climate change.

Unravelling the evolution of autumn colours: an interdisciplinary approach.

Leaf colour change is commonly observed in temperate deciduous forests in autumn. This is not simply a side effect of leaf senescence, and, in the past decade, several hypotheses have emerged to explain the evolution of autumn colours. Yet a lack of crosstalk between plant physiologists and evolutionary ecologists has resulted in slow progress, and so the adaptive value of this colour change remains a mystery. Here we provide an interdisciplinary summary of the current body of knowledge on autumn colours, and discuss unresolved issues and future avenues of research that might help reveal the evolutionary meaning of this spectacle of nature.

Autumn leaves seen through herbivore eyes.

Why leaves of some trees turn red in autumn has puzzled biologists for decades, as just before leaf fall the pigments causing red coloration are newly synthesized. One idea to explain this apparently untimely investment is that red colour signals the tree's quality to herbivorous insects, particularly aphids. However, it is unclear whether red leaves are indeed less attractive to aphids than green leaves. Because aphids lack a red photoreceptor, it was conjectured that red leaves could even be indiscernable from green ones for these insects. Here we show, however, that the colour of autumnal tree leaves that appear red to humans are on average much less attractive to aphids than green leaves, whereas yellow leaves are much more attractive. We conclude that, while active avoidance of red leaves by aphids is unlikely, red coloration in autumn could still be a signal of the tree's quality, or alternatively serve to mask the over-attractive yellow that is unveiled when the green chlorophyll is recovered from senescing leaves. Our study shows that in sensory ecology, receiver physiology alone is not sufficient to reveal the whole picture. Instead, the combined analysis of behaviour and a large set of natural stimuli unexpectedly shows that animals lacking a red photoreceptor may be able to differentiate between red and green leaves.

Photoreceptor spectral sensitivity in island and mainland populations of the bumblebee, Bombus terrestris.

Most species of flower-visiting Hymenoptera are trichromatic, with photoreceptor spectral sensitivity peaks in the UV, blue and green regions of the spectrum. Red flowers, therefore, should be relatively difficult to detect for such insects. Nevertheless, in population biological studies in the bumblebee, Bombus terrestris, the Sardinian island population (B. t. sassaricus) displayed significantly higher responses to red artificial flowers (in tests of innate colour choice and detectability) than several mainland populations of the same species (Chittka et al. in Cognitive ecology of pollination, pp 106-126, 2001; Popul Ecol 46:243-251, 2004). Since there is relatively little physiological data on population differences in sensory systems, we used intracellular recording to compare photoreceptor spectral sensitivity in B. t. sassaricus and the southern European and Mediterranean population, B. t. dalmatinus. The results show both populations to be UV-blue-green trichromats, but with a small but significant increase in long-wave sensitivity in island bees. Spectral peaks were estimated at 348, 435 and 533 nm (B. t. dalmatinus) and 347, 436 and 538 nm (B. t. sassaricus) for UV, blue and green receptors, respectively. There were no significant differences in UV and blue receptor sensitivities. We found no photoreceptors maximally sensitive to red spectral light in the Sardinian population and model calculations indicate that the behavioural population differences in colour responses cannot be directly explained by receptor population differences.